Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Dindel empty variant result file

    I'm running dindel's first stage analysis set to: getCIGARindels
    The run looks good (number of reads read is reported some indels are found, Reports "Done"), but the variant result file as well as the library file are empty.

    An idea how to fix this?

    Many thanks!

    The command, files, run log and output are listed below.





    The command I'm running is:
    dindel --analysis getCIGARindels --doDiploid --bamFile ERR024149_1_sorted.bam --outputFile out --ref chr20.fa

    The directory I set up has 4 files:
    -rw-r--r-- 1 root root 63684691 Apr 27 09:58 chr20.fa
    -rw-r--r-- 1 root root 23 Apr 27 09:58 chr20.fa.fai
    -rw-r--r-- 1 root root 799889680 Apr 27 10:01 ERR024149_1_sorted.bam
    -rw-r--r-- 1 root root 6432448 Apr 27 10:01 ERR024149_1_sorted.bam.bai

    The run messages are:
    Reading BAM file: ERR024149_1_sorted.bam
    Parsing indels from CIGAR strings...
    Wrote indels in CIGARS for target chr10 to file out
    Wrote indels in CIGARS for target chr11 to file out
    Number of reads read: 1000000
    Wrote indels in CIGARS for target chr12 to file out
    Wrote indels in CIGARS for target chr13 to file out
    Wrote indels in CIGARS for target chr14 to file out
    Number of reads read: 2000000
    Wrote indels in CIGARS for target chr15 to file out
    Wrote indels in CIGARS for target chr16 to file out
    Wrote indels in CIGARS for target chr17 to file out
    Number of reads read: 3000000
    Wrote indels in CIGARS for target chr18 to file out
    Wrote indels in CIGARS for target chr19 to file out
    Wrote indels in CIGARS for target chr1 to file out
    Number of reads read: 4000000
    Wrote indels in CIGARS for target chr20 to file out
    Wrote indels in CIGARS for target chr21 to file out
    Wrote indels in CIGARS for target chr22 to file out
    Wrote indels in CIGARS for target chr22_h2_hap1 to file out
    Number of reads read: 5000000
    Wrote indels in CIGARS for target chr2 to file out
    Wrote indels in CIGARS for target chr3 to file out
    Number of reads read: 6000000
    Wrote indels in CIGARS for target chr4 to file out
    Number of reads read: 7000000
    Wrote indels in CIGARS for target chr5 to file out
    Wrote indels in CIGARS for target chr5_h2_hap1 to file out
    Wrote indels in CIGARS for target chr6_cox_hap1 to file out
    Wrote indels in CIGARS for target chr6 to file out
    Wrote indels in CIGARS for target chr6_qbl_hap2 to file out
    Number of reads read: 8000000
    Wrote indels in CIGARS for target chr7 to file out
    Wrote indels in CIGARS for target chr8 to file out
    Number of reads read: 9000000
    Wrote indels in CIGARS for target chr9 to file out
    Wrote indels in CIGARS for target chrM to file out
    Wrote indels in CIGARS for target chrX to file out
    Wrote indels in CIGARS for target chrY to file out
    Wrote library insert sizes to out.libraries.txt
    done!


    The output files are :
    -rw-r--r-- 1 root root 0 Apr 27 10:11 ERR024149_1.dindel_output.libraries.txt
    -rw-r--r-- 1 root root 0 Apr 27 10:11 ERR024149_1.dindel_output.variants.txt

  • #2
    You shouldn't use the "--doDiploid" flag at this stage, that's for the realignment step. Not sure if that's the problem here though.

    Comment


    • #3
      You are right. I've added this flag after running without it (according to manual directions) and getting an empty variant file. It does not help to take the --doDiploid flag off.

      Comment


      • #4
        I am having the same problem of getting empty variant file from dindel. Any suggestions?
        Thanks in advance

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X